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Cheema AK, Byrum SD, Sharma NK, Altadill T, Kumar VP, Biswas S, Balgley BM, Hauer-Jensen M, Tackett AJ, Ghosh SP. Proteomic Changes in Mouse Spleen after Radiation-Induced Injury and its Modulation by Gamma-Tocotrienol. Radiat Res 2018; 190:449-463. [PMID: 30070965 PMCID: PMC6297072 DOI: 10.1667/rr15008.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Gamma-tocotrienol (GT3), a naturally occurring vitamin E isomer, a promising radioprotector, has been shown to protect mice against radiation-induced hematopoietic and gastrointestinal injuries. We analyzed changes in protein expression profiles of spleen tissue after GT3 treatment in mice exposed to gamma radiation to gain insights into the molecular mechanism of radioprotective efficacy. Male CD2F1 mice, 12-to-14 weeks old, were treated with either vehicle or GT3 at 24 h prior to 7 Gy total-body irradiation. Nonirradiated vehicle, nonirradiated GT3 and age-matched naïve animals were used as controls. Blood and tissues were harvested on days 0, 1, 2, 4, 7, 10 and 14 postirradiation. High-resolution mass-spectrometry-based radioproteomics was used to identify differentially expressed proteins in spleen tissue with or without drug treatment. Subsequent bioinformatic analyses helped delineate molecular markers of biological pathways and networks regulating the cellular radiation responses in spleen. Our results show a robust alteration in spleen proteomic profiles including upregulation of the Wnt signaling pathway and actin-cytoskeleton linked proteins in mediating the radiation injury response in spleen. Furthermore, we show that 24 h pretreatment with GT3 attenuates radiation-induced hematopoietic injury in the spleen by modulating various cell signaling proteins. Taken together, our results show that the radioprotective effects of GT3 are mediated, via alleviation of radiation-induced alterations in biochemical pathways, with wide implications on overall hematopoietic injury.
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Affiliation(s)
- Amrita K. Cheema
- Departments of Oncology, Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC
| | - Stephanie D. Byrum
- Division of Radiation Health, College of Pharmacy, University of Arkansas for Medical Sciences and Central Arkansas Veterans Healthcare System, Little Rock, Arkansas
| | - Neel Kamal Sharma
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland
| | - Tatiana Altadill
- Departments of Oncology, Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC
- Institut d’Investigacio Biomedica de Bellvitge (IDIBELL), Gynecological Department, Vall Hebron University Hospital, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Vidya P. Kumar
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland
| | - Shukla Biswas
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland
| | | | - Martin Hauer-Jensen
- Division of Radiation Health, College of Pharmacy, University of Arkansas for Medical Sciences and Central Arkansas Veterans Healthcare System, Little Rock, Arkansas
| | - Alan J. Tackett
- Division of Radiation Health, College of Pharmacy, University of Arkansas for Medical Sciences and Central Arkansas Veterans Healthcare System, Little Rock, Arkansas
| | - Sanchita P. Ghosh
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences (USUHS), Bethesda, Maryland
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Hünten S, Kaller M, Drepper F, Oeljeklaus S, Bonfert T, Erhard F, Dueck A, Eichner N, Friedel CC, Meister G, Zimmer R, Warscheid B, Hermeking H. p53-Regulated Networks of Protein, mRNA, miRNA, and lncRNA Expression Revealed by Integrated Pulsed Stable Isotope Labeling With Amino Acids in Cell Culture (pSILAC) and Next Generation Sequencing (NGS) Analyses. Mol Cell Proteomics 2015; 14:2609-29. [PMID: 26183718 DOI: 10.1074/mcp.m115.050237] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Indexed: 12/20/2022] Open
Abstract
We determined the effect of p53 activation on de novo protein synthesis using quantitative proteomics (pulsed stable isotope labeling with amino acids in cell culture/pSILAC) in the colorectal cancer cell line SW480. This was combined with mRNA and noncoding RNA expression analyses by next generation sequencing (RNA-, miR-Seq). Furthermore, genome-wide DNA binding of p53 was analyzed by chromatin-immunoprecipitation (ChIP-Seq). Thereby, we identified differentially regulated proteins (542 up, 569 down), mRNAs (1258 up, 415 down), miRNAs (111 up, 95 down) and lncRNAs (270 up, 123 down). Changes in protein and mRNA expression levels showed a positive correlation (r = 0.50, p < 0.0001). In total, we detected 133 direct p53 target genes that were differentially expressed and displayed p53 occupancy in the vicinity of their promoter. More transcriptionally induced genes displayed occupied p53 binding sites (4.3% mRNAs, 7.2% miRNAs, 6.3% lncRNAs, 5.9% proteins) than repressed genes (2.4% mRNAs, 3.2% miRNAs, 0.8% lncRNAs, 1.9% proteins), suggesting indirect mechanisms of repression. Around 50% of the down-regulated proteins displayed seed-matching sequences of p53-induced miRNAs in the corresponding 3'-UTRs. Moreover, proteins repressed by p53 significantly overlapped with those previously shown to be repressed by miR-34a. We confirmed up-regulation of the novel direct p53 target genes LINC01021, MDFI, ST14 and miR-486 and showed that ectopic LINC01021 expression inhibits proliferation in SW480 cells. Furthermore, KLF12, HMGB1 and CIT mRNAs were confirmed as direct targets of the p53-induced miR-34a, miR-205 and miR-486-5p, respectively. In line with the loss of p53 function during tumor progression, elevated expression of KLF12, HMGB1 and CIT was detected in advanced stages of cancer. In conclusion, the integration of multiple omics methods allowed the comprehensive identification of direct and indirect effectors of p53 that provide new insights and leads into the mechanisms of p53-mediated tumor suppression.
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Affiliation(s)
- Sabine Hünten
- From the ‡Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-University Munich, Thalkirchner Straβe 36, 80337 Munich, Germany
| | - Markus Kaller
- From the ‡Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-University Munich, Thalkirchner Straβe 36, 80337 Munich, Germany
| | - Friedel Drepper
- ‖Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Silke Oeljeklaus
- ‖Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Thomas Bonfert
- ‡‡Institute for Informatics, Ludwig-Maximilians-University Munich, 80337 Munich, Germany
| | - Florian Erhard
- ‡‡Institute for Informatics, Ludwig-Maximilians-University Munich, 80337 Munich, Germany
| | - Anne Dueck
- §§Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Norbert Eichner
- §§Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Caroline C Friedel
- ‡‡Institute for Informatics, Ludwig-Maximilians-University Munich, 80337 Munich, Germany
| | - Gunter Meister
- §§Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Ralf Zimmer
- ‡‡Institute for Informatics, Ludwig-Maximilians-University Munich, 80337 Munich, Germany
| | - Bettina Warscheid
- ‖Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; **Center for Biological Systems Analysis (ZBSA), University of Freiburg, 79104 Freiburg, Germany
| | - Heiko Hermeking
- From the ‡Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-University Munich, Thalkirchner Straβe 36, 80337 Munich, Germany; §German Cancer Consortium (DKTK), D-69120 Heidelberg, Germany; ¶German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany;
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Nguyen TA, Menendez D, Resnick MA, Anderson CW. Mutant TP53 posttranslational modifications: challenges and opportunities. Hum Mutat 2014; 35:738-55. [PMID: 24395704 DOI: 10.1002/humu.22506] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 01/02/2014] [Indexed: 12/13/2022]
Abstract
The wild-type (WT) human p53 (TP53) tumor suppressor can be posttranslationally modified at over 60 of its 393 residues. These modifications contribute to changes in TP53 stability and in its activity as a transcription factor in response to a wide variety of intrinsic and extrinsic stresses in part through regulation of protein-protein and protein-DNA interactions. The TP53 gene frequently is mutated in cancers, and in contrast to most other tumor suppressors, the mutations are mostly missense often resulting in the accumulation of mutant (MUT) protein, which may have novel or altered functions. Most MUT TP53s can be posttranslationally modified at the same residues as in WT TP53. Strikingly, however, codons for modified residues are rarely mutated in human tumors, suggesting that TP53 modifications are not essential for tumor suppression activity. Nevertheless, these modifications might alter MUT TP53 activity and contribute to a gain-of-function leading to increased metastasis and tumor progression. Furthermore, many of the signal transduction pathways that result in TP53 modifications are altered or disrupted in cancers. Understanding the signaling pathways that result in TP53 modification and the functions of these modifications in both WT TP53 and its many MUT forms may contribute to more effective cancer therapies.
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Affiliation(s)
- Thuy-Ai Nguyen
- Chromosome Stability Section, Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
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Wang LS, Xia L, Shen SM, Zheng Y, Yu Y, Chen GQ. Dissecting cell death with proteomic scalpels. Proteomics 2012; 12:597-606. [DOI: 10.1002/pmic.201100353] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 09/22/2011] [Accepted: 09/26/2011] [Indexed: 01/07/2023]
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Wang L, Chen G. Current advances in the application of proteomics in apoptosis research. SCIENCE CHINA-LIFE SCIENCES 2011; 54:209-19. [DOI: 10.1007/s11427-010-4123-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 05/26/2010] [Indexed: 01/18/2023]
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Pandey BN, Kumar A, Tiwari P, Mishra KP. Radiobiological basis in management of accidental radiation exposure. Int J Radiat Biol 2010; 86:613-35. [DOI: 10.3109/09553001003746059] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat Rev Genet 2009; 10:617-27. [PMID: 19687803 DOI: 10.1038/nrg2633] [Citation(s) in RCA: 314] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The systematic and quantitative molecular analysis of mutant organisms that has been pioneered by studies on mutant metabolomes and transcriptomes holds great promise for improving our understanding of how phenotypes emerge. Unfortunately, owing to the limitations of classical biochemical analysis, proteins have previously been excluded from such studies. Here we review how technical advances in mass spectrometry-based proteomics can be applied to measure changes in protein abundance, posttranslational modifications and protein-protein interactions in mutants at the scale of the proteome. We finally discuss examples that integrate proteomics data with genomic and phenomic information to build network-centred models, which provide a promising route for understanding how phenotypes emerge.
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Abu-Farha M, Elisma F, Zhou H, Tian R, Zhou H, Asmer MS, Figeys D. Proteomics: From Technology Developments to Biological Applications. Anal Chem 2009; 81:4585-99. [DOI: 10.1021/ac900735j] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mohamed Abu-Farha
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Fred Elisma
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Houjiang Zhou
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Ruijun Tian
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Hu Zhou
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Mehmet Selim Asmer
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
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Bruno M, Moore T, Nesnow S, Ge Y. Protein Carbonyl Formation in Response to Propiconazole-Induced Oxidative Stress. J Proteome Res 2009; 8:2070-8. [DOI: 10.1021/pr801061r] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maribel Bruno
- Environmental Carcinogenesis Division, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
| | - Tanya Moore
- Environmental Carcinogenesis Division, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
| | - Stephen Nesnow
- Environmental Carcinogenesis Division, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
| | - Yue Ge
- Environmental Carcinogenesis Division, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
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Playing tag with quantitative proteomics. Anal Bioanal Chem 2008; 393:503-13. [DOI: 10.1007/s00216-008-2386-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Revised: 09/01/2008] [Accepted: 09/03/2008] [Indexed: 12/27/2022]
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